git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@26 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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src/verlet.cpp
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274
src/verlet.cpp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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www.cs.sandia.gov/~sjplimp/lammps.html
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Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "string.h"
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#include "verlet.h"
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#include "neighbor.h"
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#include "domain.h"
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#include "comm.h"
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#include "atom.h"
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#include "force.h"
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#include "pair.h"
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#include "bond.h"
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#include "angle.h"
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#include "dihedral.h"
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#include "improper.h"
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#include "kspace.h"
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#include "output.h"
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#include "update.h"
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#include "modify.h"
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#include "fix.h"
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#include "timer.h"
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#include "memory.h"
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#include "error.h"
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/* ---------------------------------------------------------------------- */
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Verlet::Verlet(int narg, char **arg) : Integrate(narg, arg) {}
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/* ----------------------------------------------------------------------
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initialization before run
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------------------------------------------------------------------------- */
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void Verlet::init()
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{
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// warn if no fixes
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if (modify->nfix == 0)
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error->warning("No fixes defined, atoms won't move");
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// set flags for how virial should be computed when needed
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// pressure_flag is 1 if NPT,NPH
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// virial_every is how virial should be computed every timestep
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// 0 = not computed, 1 = computed explicity by pair,
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// 2 = computed implicitly by pair (via summation over ghost atoms)
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// virial_thermo is how virial should be computed on thermo timesteps
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// 1 = computed explicity by pair, 2 = computed implicitly by pair
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int pressure_flag = 0;
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for (int i = 0; i < modify->nfix; i++) {
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if (strcmp(modify->fix[i]->style,"npt") == 0) pressure_flag = 1;
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if (strcmp(modify->fix[i]->style,"nph") == 0) pressure_flag = 1;
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}
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if (pressure_flag && force->newton_pair) virial_every = 2;
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else if (pressure_flag) virial_every = 1;
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else virial_every = 0;
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if (force->newton_pair) virial_thermo = 2;
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else virial_thermo = 1;
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// set flags for what arrays to clear in force_clear()
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// need to clear torques if atom_style is dipole
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// need to clear phia if atom_style is granular
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// don't need to clear f_pair if atom_style is only granular (no virial)
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torqueflag = 0;
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if (atom->check_style("dipole")) torqueflag = 1;
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granflag = 0;
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if (atom->check_style("granular")) granflag = 1;
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pairflag = 1;
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if (strcmp(atom->style,"granular") == 0) pairflag = 0;
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// local versions of Update quantities
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maxpair = update->maxpair;
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f_pair = update->f_pair;
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}
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/* ----------------------------------------------------------------------
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setup before run
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------------------------------------------------------------------------- */
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void Verlet::setup()
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{
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if (comm->me == 0 && screen) fprintf(screen,"Setting up run ...\n");
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// setup domain, communication and neighboring
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// acquire ghosts
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// build neighbor lists
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domain->pbc();
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domain->reset_box();
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comm->setup();
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if (neighbor->style) neighbor->setup_bins();
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comm->exchange();
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comm->borders();
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neighbor->build();
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neighbor->ncalls = 0;
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// compute all forces
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int eflag = 1;
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int vflag = virial_thermo;
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force_clear(vflag);
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if (atom->molecular) {
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if (force->bond) force->bond->compute(eflag,vflag);
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if (force->angle) force->angle->compute(eflag,vflag);
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if (force->dihedral) force->dihedral->compute(eflag,vflag);
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if (force->improper) force->improper->compute(eflag,vflag);
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}
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if (force->pair) force->pair->compute(eflag,vflag);
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if (force->kspace) {
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force->kspace->setup();
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force->kspace->compute(eflag,vflag);
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}
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if (force->newton) comm->reverse_communicate();
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modify->setup();
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output->setup(1);
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}
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/* ----------------------------------------------------------------------
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iterate for n steps
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------------------------------------------------------------------------- */
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void Verlet::iterate(int n)
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{
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int eflag,vflag,nflag;
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for (int i = 0; i < n; i++) {
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update->ntimestep++;
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modify->initial_integrate();
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nflag = neighbor->decide();
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if (nflag == 0) {
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timer->stamp();
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comm->communicate();
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timer->stamp(TIME_COMM);
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} else {
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if (modify->n_pre_exchange) modify->pre_exchange();
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domain->pbc();
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if (domain->box_change) {
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domain->reset_box();
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comm->setup();
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if (neighbor->style) neighbor->setup_bins();
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}
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timer->stamp();
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comm->exchange();
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comm->borders();
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timer->stamp(TIME_COMM);
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if (modify->n_pre_neighbor) modify->pre_neighbor();
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neighbor->build();
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timer->stamp(TIME_NEIGHBOR);
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}
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eflag = 0;
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vflag = virial_every;
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if (output->next_thermo == update->ntimestep) {
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eflag = 1;
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vflag = virial_thermo;
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}
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force_clear(vflag);
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timer->stamp();
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if (atom->molecular) {
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if (force->bond) force->bond->compute(eflag,vflag);
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if (force->angle) force->angle->compute(eflag,vflag);
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if (force->dihedral) force->dihedral->compute(eflag,vflag);
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if (force->improper) force->improper->compute(eflag,vflag);
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timer->stamp(TIME_BOND);
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}
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if (force->pair) {
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force->pair->compute(eflag,vflag);
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timer->stamp(TIME_PAIR);
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}
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if (force->kspace) {
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force->kspace->compute(eflag,vflag);
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timer->stamp(TIME_KSPACE);
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}
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if (force->newton) {
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comm->reverse_communicate();
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timer->stamp(TIME_COMM);
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}
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if (modify->n_post_force) modify->post_force(vflag);
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modify->final_integrate();
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if (modify->n_end_of_step) modify->end_of_step();
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if (output->next == update->ntimestep) {
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timer->stamp();
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output->write(update->ntimestep);
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timer->stamp(TIME_OUTPUT);
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}
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}
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}
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/* ----------------------------------------------------------------------
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clear force on own & ghost atoms
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setup and clear other arrays as needed
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------------------------------------------------------------------------- */
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void Verlet::force_clear(int vflag)
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{
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int i;
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// clear global force array
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// nall includes ghosts only if either newton flag is set
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int nall;
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if (force->newton) nall = atom->nlocal + atom->nghost;
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else nall = atom->nlocal;
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double **f = atom->f;
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for (i = 0; i < nall; i++) {
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f[i][0] = 0.0;
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f[i][1] = 0.0;
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f[i][2] = 0.0;
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}
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if (torqueflag) {
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double **torque = atom->torque;
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for (i = 0; i < nall; i++) {
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torque[i][0] = 0.0;
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torque[i][1] = 0.0;
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torque[i][2] = 0.0;
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}
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}
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if (granflag) {
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double **phia = atom->phia;
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for (i = 0; i < nall; i++) {
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phia[i][0] = 0.0;
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phia[i][1] = 0.0;
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phia[i][2] = 0.0;
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}
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}
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// clear f_pair array if using it this timestep to compute virial
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if (vflag == 2 && pairflag) {
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if (atom->nmax > maxpair) {
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maxpair = atom->nmax;
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memory->destroy_2d_double_array(f_pair);
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f_pair = memory->create_2d_double_array(maxpair,3,"verlet:f_pair");
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update->maxpair = maxpair;
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update->f_pair = f_pair;
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}
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for (i = 0; i < nall; i++) {
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f_pair[i][0] = 0.0;
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f_pair[i][1] = 0.0;
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f_pair[i][2] = 0.0;
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}
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}
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}
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